Do the NCode™ miRNA labeling kits exhibit dye bias (green dye labels better than the red dye)?
Under the same experimental conditions, the two dyes should be labeled to the same extent with no obvious bias. However, the red dye (Alexa 5) is slightly more susceptible to photobleaching compared to the green dye (Alexa 3). Due care should be taken to protect the dyes from exposure to light. It is advisable to do a pre-scan and normalize the PMT (photomultiplier tube) gain settings to get similar signal intensities from the red and green channel. This would reduce any effect of dye bias. See related FAQ on dye swap experiments.
